P
Pavel Skums
Researcher at Georgia State University
Publications - 115
Citations - 2070
Pavel Skums is an academic researcher from Georgia State University. The author has contributed to research in topics: Population & Viral quasispecies. The author has an hindex of 18, co-authored 102 publications receiving 1356 citations. Previous affiliations of Pavel Skums include University of Connecticut & Belarusian State University.
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Journal ArticleDOI
Eleven grand challenges in single-cell data science
David Lähnemann,David Lähnemann,Johannes Köster,Johannes Köster,Ewa Szczurek,Davis J. McCarthy,Davis J. McCarthy,Stephanie C. Hicks,Mark D. Robinson,Catalina A. Vallejos,Catalina A. Vallejos,Kieran R Campbell,Kieran R Campbell,Niko Beerenwinkel,Niko Beerenwinkel,Ahmed Mahfouz,Ahmed Mahfouz,Luca Pinello,Luca Pinello,Pavel Skums,Alexandros Stamatakis,Alexandros Stamatakis,Camille Stephan Otto Attolini,Samuel Aparicio,Samuel Aparicio,Jasmijn A. Baaijens,Marleen Balvert,Marleen Balvert,Buys de Barbanson,Antonio Cappuccio,Giacomo Corleone,Bas E. Dutilh,Bas E. Dutilh,Maria Florescu,Victor Guryev,Rens Holmer,Katharina Jahn,Katharina Jahn,Thamar Jessurun Lobo,Emma M. Keizer,Indu Khatri,Szymon M. Kielbasa,Jan O. Korbel,Alexey M. Kozlov,Tzu Hao Kuo,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,Ion I. Mandoiu,John C. Marioni,John C. Marioni,John C. Marioni,Tobias Marschall,Tobias Marschall,Felix Mölder,Amir Niknejad,Lukasz Raczkowski,Marcel J. T. Reinders,Marcel J. T. Reinders,Jeroen de Ridder,Antoine-Emmanuel Saliba,Antonios Somarakis,Oliver Stegle,Oliver Stegle,Fabian J. Theis,Huan Yang,Alexander Zelikovsky,Alexander Zelikovsky,Alice C. McHardy,Benjamin J. Raphael,Sohrab P. Shah,Alexander Schönhuth,Alexander Schönhuth +71 more
TL;DR: This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years in single-cell data science.
Journal ArticleDOI
Good laboratory practice for clinical next-generation sequencing informatics pipelines
Amy S. Gargis,Lisa V. Kalman,David P. Bick,Cristina da Silva,David Dimmock,Birgit Funke,Birgit Funke,Sivakumar Gowrisankar,Sivakumar Gowrisankar,Sivakumar Gowrisankar,Madhuri Hegde,Shashikant Kulkarni,Christopher E. Mason,Rakesh Nagarajan,Karl V. Voelkerding,Karl V. Voelkerding,Elizabeth A. Worthey,Nazneen Aziz,Nazneen Aziz,John Barnes,Sarah F. Bennett,Himani Bisht,Deanna M. Church,Deanna M. Church,Zoya Dimitrova,Shaw R. Gargis,Nabil Hafez,Tina Hambuch,Fiona Hyland,Ruth Ann Luna,Duncan MacCannell,Tobias Mann,Tobias Mann,Megan R. McCluskey,Timothy K. McDaniel,Lilia Ganova-Raeva,Heidi L. Rehm,Heidi L. Rehm,Jeffrey Reid,Jeffrey Reid,David S. Campo,Richard B. Resnick,Perry G. Ridge,Perry G. Ridge,Marc L. Salit,Pavel Skums,Lee-Jun C. Wong,Barbara A. Zehnbauer,Justin M. Zook,Ira M. Lubin +49 more
TL;DR: This research highlights the need to understand more fully the role of Epstein-Barr virus in the development and management of central nervous system disorders.
Journal ArticleDOI
Efficient error correction for next-generation sequencing of viral amplicons
Pavel Skums,Zoya Dimitrova,David S. Campo,Gilberto Vaughan,Livia Maria Gonçalves Rossi,Joseph C. Forbi,Jonny Yokosawa,Alexander Zelikovsky,Yury Khudyakov +8 more
TL;DR: Two new efficient error correction algorithms optimized for viral amplicons, k-mer-based error correction (KEC) and empirical frequency threshold (ET), are presented, highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.
Journal ArticleDOI
Next-generation sequencing reveals large connected networks of intra-host HCV variants
David S. Campo,Zoya Dimitrova,Lílian Hiromi Tomonari Yamasaki,Pavel Skums,Daryl T.-Y. Lau,Gilberto Vaughan,Joseph C. Forbi,Chong-Gee Teo,Yury Khudyakov +8 more
TL;DR: Most intra-host variants are organized into distinct single-mutation components that are well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events.
Journal ArticleDOI
Accurate genetic detection of hepatitis C virus transmissions in outbreak settings
David S. Campo,Guo-liang Xia,Zoya Dimitrova,Yulin Lin,Joseph C. Forbi,Lilia Ganova-Raeva,Lili T. Punkova,Sumathi Ramachandran,Hong Thai,Pavel Skums,Seth Sims,Inna Rytsareva,Gilberto Vaughan,Ha-Jung Roh,Michael A. Purdy,Amanda Sue,Yury Khudyakov +16 more
TL;DR: A simple and accurate distance-based approach for detecting HCV transmissions streamlines molecular investigation of outbreaks, thus improving the public health capacity for rapid and effective control of hepatitis C.